Subject: New issue: Briefings in Bioinformatics, Volume 26, Issue 6, November 2025

Volume 26, Issue 6, November 2025

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News

Establishing the Asia & Pacific Bioinformatics Joint Congress: a historic milestone in regional bioinformatics collaboration

Asif M Khan and others

Papers

SLGCA: spatial cross-level graph contrastive autoencoder for multislice spatial domain identification and microenvironment exploration

Xin Lu and others

Jin Deng and others

A machine learning-based method to optimize the immunogenicity of human leukocyte antigen class I-restricted neoantigens

Jinhong Zhang and others

MOFormer: navigating the antimicrobial peptide design space with Pareto-based multi-objective transformer

Li Wang and others

Systematic evaluation of de novo mutation calling tools using whole genome sequencing data

Anushi Shah and others

BioWorkflow: Retrieving comprehensive bioinformatics workflows from publications

Yidan Wang and Jiayin Wang

DMRU: generative deep learning to unravel condition-specific cytosine methylation in plants

Sagar Gupta and others

GT-GRN: a graph transformer framework for enhanced gene regulatory network inference via multimodal embedding of expression data and existing network knowledge

Binon Teji and others

SAGE-prot: scoring-assisted generative exploration for multi-objective protein design

Hocheol Lim and others

Early cancer detection via multi-omics cfDNA fragmentation using early-late fusion neural network with sample-modality evaluation

Libo Lu and others

FGeneBERT: function-driven pre-trained gene language model for metagenomics

Chenrui Duan and others

A machine learning framework using urinary biomarkers for pancreatic ductal adenocarcinoma prediction with post hoc validation via single-cell transcriptomics

Dahlak D Solomon and others

ProjectSVR: mapping single-cell RNA-seq data to reference atlases by supported vector regression

Jianing Gao and others

BBATProt: a framework predicting biological function with enhanced feature extraction via interpretable deep learning

Youqing Wang and others

Noncoding RNA family classification based on multifeature fusion and convolutional block attention residual network

Qian Xu and others

Deep learning-based fusion of nuclear segmentation features for microsatellite instability and tumor mutational burden prediction in digestive tract cancers: a multicenter validation study

Yanping Zhang and others

Circling in on plasmids: benchmarking plasmid detection and reconstruction tools for short-read data from diverse species

Marco Teixeira and others

M³Site: multiclass multimodal learning for protein active site identification and classification

Song Ouyang and others

DSCC: disease subtyping using spectral clustering and community detection from consensus networks

Dao Tran and others

scDIFF: automatic cell type annotation using scATAC-seq data by incorporating bulk-level genomic and epigenomic information in a deep diffusive transformer

Hao-Yu Wang and others

DeepPlantAllergy: deep learning for explainable prediction of allergenicity in plant proteins

Wala Dhouib and others

CluVar: clustering of variants using autoencoder for inferring cancer subclones from single cell RNA sequencing data

Chae Won Kim and others

stTrace: detecting spatial-temporal domains from spatial transcriptome to trace developmental path

Zhangdi Song and others

CREATE: a novel attention-based framework for efficient classification of transposable elements

Yang Qi and others

BridgeNet: a high-efficiency framework integrating sequence and structure for protein and enzyme function prediction

Yilin Ye and others

PCBert-Kla: an efficient prediction method for lysine lactylation sites based on ProtBert and fusion of physicochemical features

Hong-Qi Zhang and others

Precision in prediction: tailoring machine learning models for breast cancer missense variants pathogenicity prediction

Rahaf M Ahmad and others

Accelerate the discovery of genetic variants in mitochondrial diseases with Variant prIOritization using Latent spAce

Justine Labory and others

SciSt: single-cell reference-informed spatial gene expression prediction from pathological images

Yixin Li and others

Disrupting explicit encoding paradigms: property-interactive transformers decode T-cell receptor specificity beyond dataset biases

Luming Yang and others

Fine-mapping methods for complex traits: essential adaptations for samples of related individuals

Junjian Wang and others

Evaluation of single-template ligand-based methods for the discovery of small-molecule nucleic acid binders

DÃ¡vid Bajusz and others

LogicSR: prior-guided symbolic regression for gene regulatory network inference from single-cell transcriptomics data

Dezhen Zhang and others

BridgeSyn: a bridging fusion framework for drug combination synergy prediction

Qingyu Wang and others

Introducing a foundational sequence transformer for range adaptive nucleotide decoding (STRAND)

Shant Ayanian and others

Single-cell omics arena: evaluation of large language models for automatic cell-type annotations on single-cell omics data via RNA-seq bridging

Junhao Liu and others

QTFPred: robust high-performance quantum machine learning modeling that predicts main and cooperative transcription factor bindings with base resolution

Taichi Matsubara and others

Integrating explainable artificial intelligence with multiomics systems biology and electronic health record data mining for personalized drug repurposing in Alzheimer's disease

Mohammadsadeq Mottaqi and others

Localization of macromolecules in crowded cellular cryo-electron tomograms from extremely sparse labels

Mostofa Rafid Uddin and others

Improving the predictive performance of binding affinities and poses for protein'cyclic peptide complexes through fine-tuned MM/PBSA(GBSA)-based methods

Huifeng Zhao and others

ETNet: an interpretable transformer framework for enhancer'enhancer interaction prediction with cross-context transferability

Shuaibin Wang and others

Prompt-based multimodal representation learning for drug repurposing

Jinliang Liu and others

Non-apoptotic regulated cell death based prognostic risk model for colorectal cancer using machine learning guided two-step framework

Avik Sengupta and others

Reinforcement learning with low-rank adaptation for targeted antimicrobial peptide design

Juntae Park and others

ST-GCP: a graph convolutional network model with contrastive consistency and permutation for spatial transcriptomics

Yajie Meng and others

Powerful gene network enrichment analysis and its application to severe COVID-19 gene network

Heewon Park and others

Long Noncoding RNA function prediction via multiview cross-contrastive learning combined with multiscale semantic adaptive optimization

Zhixia Teng and others

Cross-RNA transferable sequence representation learning for lncRNA m6A site detection via novel deep domain separation networks

Zhixia Teng and others

Finding coexisting combinations of posttranslational modifications with HomMTM spectra

Kunyi Li and Lusheng Wang

ProtoMol: enhancing molecular property prediction via prototype-guided multimodal learning

Yingxu Wang and others

iDNA-DAPHA: a generic framework for methylation prediction via domain-adaptive pretraining and hierarchical attention

Wenjun Wang and others

scAED: a framework for mapping the enhancer state at single-cell resolution

Avinash Veerappa and others

Comprehensive assessment of whole-genome sequencing-based variant calling pipelines in monozygotic twins

Chengyue Tan and others

SpaTM: topic models for inferring spatially informed transcriptional programs

Adrien Osakwe and others

DistRMI: a deep distance-aware neural network for explainable RNA loop motif-small molecule interaction prediction

Zhaoxiang Liu and others

STIFT: spatiotemporal transcriptomics integration through spatially informed multi-timepoint bridging

Ji Qi and others

PBIP: a deep learning framework for predicting phage'bacterium interactions at the strain level

Lijia Ma and others

HuAbDiffusion: a discrete language diffusion model used for antibody humanization

Dongping Liu and others

Strategies for community-sourced biocuration in bioinformatics: a case study on MIBiG 4.0

Kai Blin and others

Impact of intrinsically disordered regions and functional disorder hotspots in the human kinome

Sonet Daniel Thomas and others

PLiCat: decoding protein'lipid interactions by large language model

Feitong Dong and Jingrou Wu

Identification of the body fluid donors from mixture stains using bulk transcriptomes data

Huan Yu and others

Generating three-dimensional genome structures with a variational quantum algorithm

Andrew Jordan Siciliano and Zheng Wang

Decoupled dual-granularity rebalanced pyramid network for drug'target interaction prediction

Zhiyuan Dong and others

Benchmarking large language models for cell typing in single-cell RNA-Seq

Tianxiang Xiao and others

scHLens: a web server for hierarchically and interactively exploring single cell RNA-seq data

Jiazhi Xia and others

Identification of key candidate genes for ovarian cancer using integrated statistical and machine learning approaches

Md Ali Hossain and others

graphB³'an interpretable graph learning approach for predicting blood'brain barrier permeability

Sumit Kumar and others

Prediction of liquid'liquid phase separation proteins based on protein language model

Wenbin Li and others

Few-shot drug synergy prediction via rapid cross-tier adaptation meta-optimization

Yue-Hua Feng and others

Benchmarking single-sample gene set scoring methods for application in precision medicine

Daniel Toro-DomÃnguez and others

Multi-omics data integration for enhanced cancer subtyping via interactive multi-kernel learning

Hongyan Cao and others

IgRENE: integrating gene regulatory networks and drug ontologies towards selected modification of target gene's expression

George Minadakis and George M Spyrou

Structure-enhanced deep learning accelerates aptamer selection for small molecule families like steroids

Zibin Zhao and others

Component puzzle protein'protein interaction prediction

SeyedMohsen Hosseini and others

Probabilistic-graph-based spatial context-aware framework for interpretable spatial omics denoising and augmentation

Xianhan Qin and others

Deciphering RNA modification and post-transcriptional regulation with NetRNApan

Haodong Xu and others

Protrec2: tissue-specific network-based missing protein recovery method

Weijia Kong and others

CELLetter: leveraging large language model and dual-stream network to identify context-specific ligand'receptor interactions for cell'cell communication analysis

Wei Wu and others

Proformer: a multimodal proteomics transformer model for multidisease early risk assessment

Shizheng Qiu and others

MetImputBERT: a pretrained BERT framework for missing value imputation in NMR metabolomics data

Shizheng Qiu and others

MOGEDN: small-sample cancer subtype classification with encoder'decoder networks for missing-omics recovery and biomarker discovery

Dingnan Jin and Yutaka Saito

DeepADR: multimodal prediction of adverse drug reaction frequency by integrating early-stage drug discovery information via Kolmogorov'Arnold networks

Jingting Wan and others

Case Studies

Decoding heart failure subtypes with neural networks via differential explanation analysis

Mariano Ruz Jurado and others

SynOmics: integrating multi-omics data through feature interaction networks

Muhtasim Noor Alif and Wei Zhang

Advancing toxicity AI-based prediction with multilevel systems biology: a case study on genotoxicity

Xin Zhang and others

MFE-ACVP: anti-coronavirus peptide prediction based on multimodal feature extraction and ensemble learning

Liqiong Kang and others

Decoding protein N-phosphorylation functionality and sequence patterns

Ming-Xiao Zhao and others

Large-scale multi-trait genome-wide analysis for inflammatory bowel disease reveals new insights into its molecular mechanisms and emphasizes the roles of systemic immune regulation

Zijun Zhu and others

Systematic identification and characterization of virus lncRNAs suggests extensive structural mimicry of host lncRNAs

Ping Fu and others

Using a consensus machine learning approach to identify host biomarkers associated with treatment response in pulmonary tuberculosis

Ruiqi Zhang and others

Systematic evaluation of predictors for binding free energy changes upon mutations in protein complexes

Yu Zhang and others

KmerCrypt: private k-mer search with homomorphic encryption

Kimonas Provatas and others

Letter to Editor

Response to ˜Methodological and statistical concerns in MINERVA microbiome'disease knowledge graph' by Salvatore Chirumbolo

Saul Langarica and others

Methodological and statistical concerns in MINERVA microbiome-disease knowledge graph

Salvatore Chirumbolo

Corrections

Correction to: DriverOmicsNet: an integrated graph convolutional network for multi-omics exploration of cancer driver genes

Correction to: Computational toxicology in drug discovery: applications of artificial intelligence in ADMET and toxicity prediction

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